> library(flexdashboard)

> library(rio)

> library(tidyverse)

> library(XML)

> library(httr)

> library(RCurl)

> library(sf)

> library(lubridate)

> library(leaflet)

> library(colorspace)

> library(DT)

> library(zoo)

> library(slider)

> library(plotly)

> library(waffle)

> library(extrafont)

> library(plyr)

> library(extrafont)

> library(waffle)

> library(RColorBrewer)

> library(leaflet.extras)

> library(rmapshaper)

> options(scipen = 999)

> plotly_mod_dep = function(p) {
+     deps <- p$dependencies
+     deps_urls <- purrr::map(deps, ~if (.x$name == "plotly-basic") {
+         .x$src = .... [TRUNCATED] 

---
title: "CE4 - Dashboard COVID-19"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
    source_code: embed
    social: menu
    theme: cosmo
    self_contained: FALSE 
    fig_mobile: TRUE
---



```{r libraries}
source('func_lib.R', echo = TRUE)

```

```{r imports}
nac <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true")

deps <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true", sheet = 2)

pop <- read_csv("data/peru_pop_stratum.csv") %>%
  group_by(dep_adm1) %>%
  dplyr::summarise(pop = sum(N)) %>%
  dplyr::mutate(REGION = toupper(dep_adm1))


Paises_LATAM <- c("Argentina","Bolivia","Brazil","Chile","Colombia","Ecuador","Mexico","Peru","Uruguay","Venezuela")
LATAM <- read_csv ("https://covid.ourworldindata.org/data/owid-covid-data.csv") %>%
  dplyr::filter(location %in% Paises_LATAM) %>%
  dplyr::mutate( mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6))

```

```{r dm maps, include=FALSE}
c.date <- max(deps$Fecha)
y.date <- as.Date(c.date) - 1 

dep <- 
  deps %>% 
  dplyr::select(dat = Fecha,
                dep = REGION, 
                pos = Positivos_totales, 
                pos.imp = PositivosImputados_totales,
                pas =Fallecidos, 
                smp =Total_muestras) %>% 
  dplyr::mutate(pas = pas %>% if_else(is.na(.), 0, .)) %>% 
  group_by(dep) %>% 
  dplyr::mutate(pos.lag = lag(pos, n = 1),
                pos.imp.lag = lag(pos.imp, n = 1),
                pas.lag = lag(pas, n = 1),
                smp.lag = lag(smp, n = 1)) %>%
  dplyr::filter(dat == c.date) %>% 
  dplyr::mutate(pos.new = abs(pos - pos.lag),
                pos.imp.new = abs(pos.imp - pos.imp.lag),
                pas.new = abs(pas - pas.lag),
                smp.new = abs(smp - smp.lag),
                ratio.new = signif(pos.new/smp.new), digits = 3,
                pos.new.log = log(pos.new),
                pas.new.log = log(pas.new)) %>% 
  mutate(pos.new.log = replace(pos.new.log, pos.new == 0, 0),
         pas.new.log = replace(pas.new.log, pas.new == 0, 0))


y.dep <- 
  deps %>% 
  dplyr::select(dat = Fecha,
                dep = REGION, 
                pos = Positivos_totales, 
                pos.imp = PositivosImputados_totales,
                pas =Fallecidos, 
                smp =Total_muestras) %>% 
  dplyr::mutate(pas = pas %>% if_else(is.na(.), 0, .)) %>% 
  group_by(dep) %>% 
  dplyr::mutate(pos.lag = lag(pos, n = 1),
                pos.imp.lag = lag(pos.imp, n = 1),
                pas.lag = lag(pas, n = 1),
                smp.lag = lag(smp, n = 1)) %>%
  dplyr::filter(dat == y.date) %>% 
  dplyr::mutate(pos.new = abs(pos - pos.lag),
                pos.imp.new = abs(pos.imp - pos.imp.lag),
                pas.new = abs(pas - pas.lag),
                smp.new = abs(smp - smp.lag),
                ratio.new = signif(pos.new/smp.new), digits = 3)

## Regions geometry
shp <- st_read("Limite_departamental", stringsAsFactors = F)
shp <- shp %>% 
  st_transform(4326) %>% 
  select(Departamento = NOMBDEP) %>%
  rmapshaper::ms_simplify()

# Append
dep <- merge(dep, shp, by.y = 'Departamento', by.x = 'dep', all.x = T)
dep <- st_as_sf(dep, sf_column_name = 'geometry')
dep <- merge(dep, pop %>% select(dep = REGION, pop))
dep <- dep %>% mutate(pos.hab = pos/pop*100000, 
                      smp.hab = smp/pop*100000)
```

```{r dm, message=F, warning=F}
today <- ymd(Sys.Date())

deps1 <- deps %>%
  dplyr::select(REGION, Fecha, Positivos_totales, Positivos_PR,PositivosImputados_totales) %>% 
  inner_join(pop, by="REGION") %>%
  arrange(REGION, Fecha) %>%
  group_by(REGION) %>%
  dplyr::mutate(new_cases = Positivos_totales - lag(Positivos_totales, default = 0),
                new_cases_inp = PositivosImputados_totales - lag(PositivosImputados_totales, default = 0),
                mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6),
                pmav_new = 1000000*mav_new/pop,
                max = max(mav_new),
                dias = as.numeric(Fecha-first(Fecha), unit="days")) %>%
  mutate(tm = difftime(today, Fecha , units = c("days")))

nac1 <- nac %>%
  dplyr::mutate(RapidasPositivos = replace_na(RapidasPositivos,0),
                Descartados = replace_na(Descartados,0),
                PruebasRapidas = replace_na(PruebasRapidas,0),
                total_pos = Positivos + RapidasPositivos,
                pos_new = total_pos -lag(total_pos,default = 0),
                rapid_des = PruebasRapidas - RapidasPositivos,
                total_des = rapid_des + Descartados,
                des_new = total_des-lag(total_des,default = 0),
                Dia = ymd(Dia)) %>%
  dplyr::select(Dia,
                pos_new,
                des_new) %>%
  dplyr::mutate(cum_pos = cumsum(pos_new),
                tot_pruebas = pos_new+des_new,
                tm = difftime(today, Dia , units = c("days")))


nac2 <- nac1 %>%
  dplyr::mutate(neg_new = tot_pruebas-pos_new) %>%
  dplyr::select(Dia, pos_new, neg_new) %>%
  dplyr::rename(Positivo = pos_new, Negativo = neg_new) %>%
  gather(res, count, -Dia) %>%
  uncount(count)

nac3 <- nac1 %>%
  dplyr::mutate(new_cases = cum_pos - lag(cum_pos, default = 0),
                mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6),
                max = max(mav_new)
  )

deps2_10 <- deps1 %>%
  dplyr::filter(REGION %in%(deps1 %>% group_by(REGION) %>% 
                              dplyr::summarise(max = as.numeric(max(max)))%>% 
                              dplyr::arrange(dplyr::desc(max)) %>%
                              top_n(10) %>% dplyr::pull(REGION))) %>%
  select(Fecha,REGION,mav_new) %>%
  spread(REGION, mav_new) %>%
  mutate(tm = difftime(today, Fecha , units = c("days"))) %>%
  plyr::rename(replace= c(`LA LIBERTAD` = "LA_LIBERTAD",
                          `MADRE DE DIOS` = "MADRE_DE_DIOS",
                          `SAN MARTIN` = "SAN_MARTIN"),
               warn_missing = FALSE)


deps2_25 <- deps1 %>%
  dplyr::filter(!(REGION %in%(deps1 %>% group_by(REGION) %>% 
                                dplyr::summarise(max = as.numeric(max(max)))%>% 
                                dplyr::arrange(dplyr::desc(max)) %>%
                                top_n(10) %>% dplyr::pull(REGION)))) %>%
  select(Fecha,REGION,mav_new) %>%
  spread(REGION, mav_new) %>%
  mutate(tm = difftime(today, Fecha , units = c("days")))%>%
  plyr::rename(replace= c(`LA LIBERTAD` = "LA_LIBERTAD",
                          `MADRE DE DIOS` = "MADRE_DE_DIOS",
                          `SAN MARTIN` = "SAN_MARTIN"),
               warn_missing = FALSE)

deps3_10 <- deps1 %>%
  dplyr::filter(REGION %in%(deps1 %>% group_by(REGION) %>% 
                              dplyr::summarise(max = as.numeric(max(max)))%>% 
                              dplyr::arrange(dplyr::desc(max)) %>%
                              top_n(10) %>% dplyr::pull(REGION))) %>%
  select(Fecha,REGION,pmav_new) %>%
  spread(REGION, pmav_new) %>%
  mutate(tm = difftime(today, Fecha , units = c("days"))) %>%
  plyr::rename(replace= c(`LA LIBERTAD` = "LA_LIBERTAD",
                          `MADRE DE DIOS` = "MADRE_DE_DIOS",
                          `SAN MARTIN` = "SAN_MARTIN"),
               warn_missing = FALSE)


deps3_25 <- deps1 %>%
  dplyr::filter(!(REGION %in%(deps1 %>% group_by(REGION) %>% 
                                dplyr::summarise(max = as.numeric(max(max)))%>% 
                                dplyr::arrange(dplyr::desc(max)) %>%
                                top_n(10) %>% dplyr::pull(REGION)))) %>%
  select(Fecha,REGION,pmav_new) %>%
  spread(REGION, pmav_new) %>%
  mutate(tm = difftime(today, Fecha , units = c("days")))%>%
  plyr::rename(replace= c(`LA LIBERTAD` = "LA_LIBERTAD",
                          `MADRE DE DIOS` = "MADRE_DE_DIOS",
                          `SAN MARTIN` = "SAN_MARTIN"),
               warn_missing = FALSE)

deps2 <- deps1 %>%
  select(Fecha,REGION,mav_new) %>%
  spread(REGION, mav_new) %>%
  mutate(tm = difftime(today, Fecha , units = c("days"))) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

deps3 <- deps1 %>%
  select(Fecha,REGION,pmav_new) %>%
  spread(REGION, pmav_new) %>%
  mutate(tm = difftime(today ,Fecha , units = c("days"))) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

deps4 <- deps1 %>% #Distinto a deps2
  select(Fecha,REGION,new_cases_inp) %>%
  spread(REGION, new_cases_inp) %>%
  mutate(tm = difftime(today, Fecha , units = c("days")))%>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 



nac4 <- nac1 %>%
  dplyr::mutate(dias = as.numeric(Dia-first(Dia), unit="days"),
                calc = dias+20,
                dup_1 = exp((log(2)/1)*dias),
                dup_2 = exp((log(2)/2)*dias),
                dup_3 = exp((log(2)/3)*dias),
                dup_4 = exp((log(2)/4)*dias)
  )

nac5 <- nac%>%
  dplyr::mutate(RapidasPositivos = replace_na(RapidasPositivos,0),
                Descartados = replace_na(Descartados,0),
                PruebasRapidas = replace_na(PruebasRapidas,0),
                total_pos = Positivos + RapidasPositivos,
                pos_new = total_pos -lag(total_pos,default = 0),
                Dia = ymd(Dia),
                Recuperados = ifelse(is.na(Recuperados),0,Recuperados),
                Fallecidos = ifelse(is.na(Fallecidos),0,Fallecidos),
                Activos = cumsum(pos_new)-(Recuperados+Fallecidos),
                Total = Recuperados + Fallecidos + Activos,
                per_recuperados =Recuperados/Total,
                per_fallecidos =Fallecidos/Total,
                per_activos = Activos/Total)%>% 
  dplyr::select(Dia,pos_new,Recuperados,Fallecidos,Activos,Total,per_recuperados,per_fallecidos,per_activos)

icon_svg_path <-"M12.871,9.337H7.377c-0.304,0-0.549,0.246-0.549,0.549c0,0.303,0.246,0.55,0.549,0.55h5.494c0.305,0,0.551-0.247,0.551-0.55C13.422,9.583,13.176,9.337,12.871,9.337z M15.07,6.04H5.179c-0.304,0-0.549,0.246-0.549,0.55c0,0.303,0.246,0.549,0.549,0.549h9.891c0.303,0,0.549-0.247,0.549-0.549C15.619,6.286,15.373,6.04,15.07,6.04z M17.268,1.645H2.981c-0.911,0-1.648,0.738-1.648,1.648v10.988c0,0.912,0.738,1.648,1.648,1.648h4.938l2.205,2.205l2.206-2.205h4.938c0.91,0,1.648-0.736,1.648-1.648V3.293C18.916,2.382,18.178,1.645,17.268,1.645z M17.816,13.732c0,0.607-0.492,1.1-1.098,1.1h-4.939l-1.655,1.654l-1.656-1.654H3.531c-0.607,0-1.099-0.492-1.099-1.1v-9.89c0-0.607,0.492-1.099,1.099-1.099h13.188c0.605,0,1.098,0.492,1.098,1.099V13.732z"

roundUpNice <- function(x, nice=c(1,2,5,6,10)) {
  if(length(x) != 1) stop("'x' must be of length 1")
  10^floor(log10(x)) * nice[[which(x <= 10^floor(log10(x)) * nice)[[1]]]]
}
```

Nacional {.bg}
=====================================  

Column 1 {.tabset data-width=350} 
-------------------------------------

### Casos

```{r}
labels.total <- sprintf(
  "%s
Casos: %s",
  dep$dep, dep$pos) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette="RdPu", domain = log(dep$pos), na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.cases(log(dep$pos)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.total,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal = pal.cases, values = log(dep$pos), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121)%>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra los casos acumulados por departamento. El gradiente de colores indica mayor casos acumulados en colores más oscuros.');
    }")))  %>%
  suspendScroll(sleep = TRUE, sleepTime = 750, wakeTime = 750,
  sleepNote = TRUE, hoverToWake = F,
  wakeMessage = "Click para utilizar el mapa", sleepOpacity = 0.7)

  
```

### Casos / 100k hab

```{r}
labels.pos.hab <- sprintf(
  "%s
Casos/100k hab: %s",
  dep$dep, round(dep$pos.hab)) %>% lapply(htmltools::HTML)

pal.pos.hab <- colorNumeric( palette="RdPu", domain = log(dep$pos.hab), na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.pos.hab(log(dep$pos.hab)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.pos.hab,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal = pal.pos.hab, values = log(dep$pos.hab), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121)%>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra la tasa de casos por 100 mil habitantes por departamento. El gradiente de colores indica mayor tasa de casos en colores más oscuros.');
    }")))  %>%
  suspendScroll(sleep = TRUE, sleepTime = 750, wakeTime = 750,
  sleepNote = TRUE, hoverToWake = F,
  wakeMessage = "Click para utilizar el mapa", sleepOpacity = 0.7)

  
```

### Casos nuevos 

```{r}
labels.new <- sprintf(
  "%s
Casos: %s",
  dep$dep, dep$pos.new) %>% lapply(htmltools::HTML)

pal.newcases <- colorNumeric( palette="RdPu", domain = dep$pos.new.log, na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.newcases(dep$pos.new.log),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.new,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.newcases, values = dep$pos.new.log, title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121) %>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra los casos nuevos por departamento. El gradiente de colores indica mayor cantidad de casos nuevos en colores más oscuros. Departamentos sin color no han reportado casos nuevos.');
    }")))  %>%
  suspendScroll(sleep = TRUE, sleepTime = 750, wakeTime = 750,
  sleepNote = TRUE, hoverToWake = F,
  wakeMessage = "Click para utilizar el mapa", sleepOpacity = 0.7)
 



```

### Fallecidos 

```{r}
labels.pas <- sprintf(
  "%s
Fallecidos: %s",
  dep$dep, dep$pas) %>% lapply(htmltools::HTML)

pal.pas <- colorNumeric( palette="RdPu", domain = dep$pas, na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.pas(dep$pas),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.pas,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.pas, values = dep$pas, title= 'Fallecidos')%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121) %>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra el total de fallecidos por departamento. El gradiente de colores indica mayor total de fallecidos en colores más oscuros.');
    }")))  %>%
  suspendScroll(sleep = TRUE, sleepTime = 750, wakeTime = 750,
  sleepNote = TRUE, hoverToWake = F,
  wakeMessage = "Click para utilizar el mapa", sleepOpacity = 0.7)

 
```

### Fallecidos nuevos

```{r}
labels.pasnew <- sprintf(
  "%s
Fallecidos: %s",
  dep$dep, dep$pas.new) %>% lapply(htmltools::HTML)

pal.pasnew <- colorNumeric( palette="RdPu", domain = dep$pas.new, na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.pasnew(dep$pas.new),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.pasnew,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.pasnew, values = dep$pas.new, title= 'Fallecidos')%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121) %>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra número de fallecidos nuevos por departamento. El gradiente de colores indica mayor número fallecidos nuevos en colores más oscuros.');
    }")))  %>%
  suspendScroll(sleep = TRUE, sleepTime = 750, wakeTime = 750,
  sleepNote = TRUE, hoverToWake = F,
  wakeMessage = "Click para utilizar el mapa", sleepOpacity = 0.7)

```

### Pruebas

```{r}
labels.smp <- sprintf(
  "%s
Pruebas: %s",
  dep$dep, dep$smp) %>% lapply(htmltools::HTML)

pal.smp <- colorNumeric( palette="Blues", domain = log(dep$smp), na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.smp(log(dep$smp)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.smp,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.smp, values = log(dep$smp), title= 'Pruebas', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121)%>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra el total pruebas realizadas por departamento. El gradiente de colores indica mayor total de pruebas realizadas en colores más oscuros.');
    }")))  %>%
  suspendScroll(sleep = TRUE, sleepTime = 750, wakeTime = 750,
  sleepNote = TRUE, hoverToWake = F,
  wakeMessage = "Click para utilizar el mapa", sleepOpacity = 0.7)
```

### Pruebas / 100k hab

```{r}
labels.smp.hab <- sprintf(
  "%s
Pruebas/100k hab: %s",
  dep$dep, round(dep$smp.hab)) %>% lapply(htmltools::HTML)

pal.smp.hab <- colorNumeric( palette="Blues", domain = log(dep$smp.hab), na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.smp.hab(log(dep$smp.hab)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.smp.hab,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.smp.hab, values = log(dep$smp.hab), title= 'Pruebas', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121)   %>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra la tasa de pruebas realizadas por 100 mil habitantes por departamento. El gradiente de colores indica mayor tasa de pruebas por 100 mil habitantes realizadas en colores más oscuros.');
    }"))) %>%
  suspendScroll(wakeMessage = "Click para utilizar el mapa")
```

### Nuevas pruebas

```{r}
labels.smp.new <- sprintf(
  "%s
Pruebas: %s",
  dep$dep, dep$smp.new) %>% lapply(htmltools::HTML)

pal.smpnew <-  colorNumeric( palette="Blues", domain = log(dep$smp.new), na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor =pal.smpnew(log(dep$smp.new)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.smp.new,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.smpnew, values = log(dep$smp.new), title= 'Pruebas', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121)  %>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra número de nuevas pruebas realizadas por departamento. El gradiente de colores indica mayor número de pruebas realizadas en colores más oscuros.');
    }"))) %>%
  suspendScroll(sleep = TRUE, sleepTime = 750, wakeTime = 750,
  sleepNote = TRUE, hoverToWake = F,
  wakeMessage = "Click para utilizar el mapa", sleepOpacity = 0.7)
```

### Tasa de positivos nuevos

```{r}
labels.ratio <- sprintf(
  "%s
Porcentaje: %s",
  dep$dep, dep$ratio.new*100) %>% lapply(htmltools::HTML)

pal.ratio <-  colorNumeric( palette="RdPu", domain = dep$ratio.new*100, na.color="transparent")

leaflet(dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.ratio(dep$ratio.new*100),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.ratio,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.ratio, values = dep$ratio.new*100, title= '% Positivos')%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121) %>%
  addEasyButton(easyButton(
    icon="fa-info-circle", title="Información",
    onClick=JS("function(gd) { 
      alert('Muestra proporción de pruebas positivas entre todas las pruebas nuevas realizadas por departamento. El gradiente de colores indica mayor proporción de pruebas positivas en colores más oscuros.');
    }"))) %>%
  suspendScroll()
```

Column 2 {.tabset data-width=400 vertical_layout=scroll}
-------------------------------------

### Lineal

```{r, message=F, warning=F}
infobutton_1 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra los casos nuevos por día (barras) y casos acumulados (línea naranja) en escala lineal a nivel nacional. La escala lineal sirve para visualizar la suma contínua de casos.');
    }"
  )
)
####
plot_ly(nac1) %>%
  add_trace(x = ~Dia, y = ~pos_new, 
            type = 'bar', name = 'Casos nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~Dia, y = ~cum_pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos acumulados', 
            yaxis = 'y2',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Acumulados: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac1$pos_new),
               text="2020-04-08",name="Inicio de Pruebas Rápidas",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = 'Casos nuevos y acumulados - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de Reporte",
                      color = "white",
                      tickformat= "%d-%b"),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', 
                      showgrid = T, gridcolor = "#818181", zeroline = F,
                      color = "#98cbe1",
                      range=list(0, roundUpNice(max(nac1$pos_new))),
                      autotick=F,
                      tick0=0,
                      dtick=roundUpNice(max(nac1$pos_new))/5),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Casos acumulados por día (lineal)', 
                       showgrid = F, zeroline = F,
                       color = "#ffd29f",
                       range=list(0, roundUpNice(max(nac1$cum_pos))),
                       autotick=F,
                       tick0=0,
                       dtick=roundUpNice(max(nac1$cum_pos))/5),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=65, b=40, t=50),
         autosize=T
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_1),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')

```

### Logaritmico

```{r, message=F, warning=F}

infobutton_2 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra los casos nuevos por día (barras) y casos acumulados (línea naranja) en escala logarítmica a nivel nacional. La escala logarítmica sirve para visualizar la multiplicación de los casos y observar si la curva se aplana.');
    }"
  )
)

plot_ly(nac1) %>%
  add_trace(x = ~Dia, y = ~pos_new, 
            type = 'bar', name = 'Casos nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~Dia, y = ~cum_pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados', 
            yaxis = 'y2',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Acumulados: %{y:.0f}
",
                                   '%{text}')) %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac1$pos_new),
               text="2020-04-08",name="Inicio de Pruebas Rápidas",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  ) %>% 
  layout(title = 'Casos nuevos y acumulados - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color ="white",
                      tickformat= "%d-%b",
                      range = c(as.Date("2020-03-06"),
                                as.Date(c.date))),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', 
                      showgrid = T, gridcolor = "#818181", zeroline = F,
                      color = "#98cbe1",
                      range=list(0, roundUpNice(max(nac1$pos_new))),
                      autotick=F,
                      tick0=0,
                      dtick=roundUpNice(max(nac1$pos_new))/5),
         yaxis2 = list(side = 'right', overlaying = "y", type = "log",
                       title = 'Casos acumulados (logaritmica)', 
                       showgrid = F, zeroline = F,
                       color = "#ffd29f",
                       range=list(0, 5),
                       autotick=F,
                       tick0=0),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=65, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_2),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')
```

### Media Móvil


```{r, message=F, warning=F}
infobutton_3 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra los casos nuevos por día (barras) y la media móvil (línea naranja) a 7 días a nivel nacional. La media móvil muestra el valor promedio de los casos reportados en un periodo determinado.');
    }"
  )
)

plot_ly(nac3) %>%
  add_trace(x = ~Dia, y = ~pos_new,
            type = 'bar', name = 'Casos nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac3$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~Dia, y = ~mav_new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Media Móvil',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac3$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Media móvil: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac3$pos_new),
               text="2020-04-08",name="Inicio de Pruebas Rápidas",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = 'Media móvil (7d) y casos nuevos por día - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color="white",
                      tickformat= "%d-%b",
                      range = c(as.Date("2020-03-06"),
                                as.Date(c.date))),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', 
                      showgrid = T, gridcolor = "#818181", zeroline = F,
                      color = "#98cbe1",
                      range=list(0, roundUpNice(max(nac3$pos_new))),
                      autotick=F,
                      tick0=0,
                      dtick=roundUpNice(max(nac3$pos_new))/5),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Media móvil de casos nuevos - 7 días (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color="#ffa600",
                       range = c(min(0),
                                 max(nac3$pos_new))),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.15,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=0, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_3),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')

```

### Duplicación

```{r, message=F, warning=F}
infobutton_4 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra los casos acumulados en escala logarítmica desde el día del primer reporte a nivel nacional. Las líneas punteadas corresponden a las pendientes de duplicación de casos cada 1 a 4 días; una pendiente más inclinada implica la duplicación de casos en menor tiempo.');
    }"
  )
)

x <- data.frame(Dia = as.Date(seq(1,30, 1)+today)  )


y <- x %>%
  dplyr::mutate(dias = as.numeric(Dia-first(nac4$Dia), unit="days"),
                calc = dias+20,
                dup_1 = exp((log(2)/1)*dias),
                dup_2 = exp((log(2)/2)*dias),
                dup_3 = exp((log(2)/3)*dias),
                dup_4 = exp((log(2)/4)*dias)
  ) %>%
  bind_rows(nac4)

plot_ly(y)%>%
  add_trace(x = ~dias, y = ~cum_pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1') %>% 
  add_trace(x = ~dias, y = ~dup_1,
            mode = 'lines', 
            name = 'Casos se duplican en un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_2,
            mode = 'lines', 
            name = 'Casos se duplican en dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_3,
            mode = 'lines', 
            name = 'Casos se duplican en tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_4,
            mode = 'lines', 
            name = 'Casos se duplican en cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en cuatro (4) días",
            hoverinfo = "text",
            legendgroup = 'group2')  %>% 
  layout(title = 'Total de casos acumulados desde el inicio de los casos',
         titlefont=list(color="white"),
         xaxis = list(title = "Días desde el primer reporte",
                      range = c(min(0),max(nac4$calc)+5),
                      color ="white"),
         yaxis = list(side = 'left', 
                      title = list(text= 'Total de casos acumulados', 
                                   font = list(size = 16,
                                               color = "White"),
                                   standoff = 15),   
                      type="log", automargin = T,
                      range = c(min(0),max(6)), 
                      showgrid = T, gridcolor = "#818181", zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="ffd29f"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.25,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=30, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_4),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')


```


### Según estado
```{r, message=F, warning=F}
infobutton_5 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra la proporción de casos acumulados según estado en escala lineal a nivel nacional.');
    }"
  )
)

fig <- plot_ly(nac5, x = ~Dia)

fig <- fig %>% add_trace( y = ~Fallecidos, name = 'Fallecidos', 
                          type = 'scatter', mode = 'lines+markers',
                          marker = list(color =  'rgba(0,0,0,0)'),
                          line = list(color = '#ffa600'), 
                          stackgroup = 'one', fillcolor = '#ffa600')

fig <- fig %>% add_trace(y = ~Recuperados, 
                         name = 'Recuperados', fillcolor = '#7aa82a',
                         marker = list(color =  '#7aa82a'),
                         line = list(color = '#7aa82a'), 
                         stackgroup = 'one')

fig <- fig %>% add_trace(y = ~Activos, 
                         name = 'Activos', mode = 'none', 
                         fillcolor = '#035871',
                         marker = list(color = '#0e5871'),
                         line = list(color = '#0e5871'), 
                         stackgroup = 'one')

fig <- fig %>% 
  layout(title ="Proporción de casos Activos, Recuperados, y Fallecidos",
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      showgrid = FALSE,
                      color ="white"),
         yaxis = list(title = "Número de casos según estado",
                      showgrid = FALSE,
                      color ="white"),
         paper_bgcolor="black",
         plot_bgcolor="black",
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=25, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_5),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')


fig
```

### Proporción de casos
```{r, message=F, warning=F}
infobutton_6 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra la proporción de casos acumulados según estado a nivel nacional.' 
);
    }"
  )
)

fig <- plot_ly(nac5, x = ~Dia, y = ~per_fallecidos, name = 'Fallecidos', 
               type = 'scatter', mode = 'lines+markers', stackgroup = 'one', 
               groupnorm = 'percent', fillcolor = '#ffa600',
               marker = list(color =  'rgba(0,0,0,0)'),
               line = list(color = '#bbac00'),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Fallecidos: %{y:.2f}%
"))

fig <- fig %>% add_trace(y = ~per_recuperados, 
                         name = 'Recuperados', fillcolor = '#7aa82a',
                         marker = list(color =  'rgba(0,0,0,0)'),
                         line = list(color = '#7aa82a'),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Recuperados: %{y:.2f}%
"))

fig <- fig %>% add_trace(y = ~per_activos, 
                         name = 'Activos', mode = 'none', 
                         fillcolor = '#035871',
                         marker = list(color = 'rgba(0,0,0,0)'),
                         line = list(color = 'rgba(0,0,0,0)'),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Activos: %{y:.2f}%
"))

fig <- fig %>% 
  layout(title ="Proporción de casos Activos, Recuperados, y Fallecidos",
         titlefont=list(color="white"),
         shapes = list(
           list(
             type = "line", 
             x0 = 0, x1 = 1, 
             xref = "paper",
             y0 = 50, y1 = 50, 
             line = list(color = "white", 
                         dash = "dash")
           ),
           list(
             type = "line", 
             x0 = 0, x1 = 1, 
             xref = "paper",
             y0 = 25, y1 = 25, 
             line = list(color = "white", 
                         dash = "dot")
           ),
           list(
             type = "line", 
             x0 = 0,  x1 = 1, 
             xref = "paper",
             y0 = 75, y1 = 75, 
             line = list(color = "white", 
                         dash = "dot")
           )
         ),
         xaxis = list(title = "Fecha de reporte",
                      showgrid = FALSE,
                      color ="white"),
         yaxis = list(title = "Proporción de casos según estado",
                      showgrid = FALSE,
                      ticksuffix = '%',
                      color ="white"),
         paper_bgcolor="black",
         plot_bgcolor="black",
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=25, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_5),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')

fig
```

Column 3 {data-width=250}
-------------------------------------

### `r c.date` 
```{r}
valueBox("Datos actualizados al:", icon = "fa-calendar", color = 'teal')
```

### `r paste0(format(sum(dep$pos, na.rm = T), big.mark = ","), ' Casos en las últimas 24 horas')`

```{r}
if (sum(dep$pos.new, na.rm = T) > sum(y.dep$pos.new, na.rm = T)) {
  valueBox(paste0(format(sum(dep$pos.new, na.rm = T), big.mark = ","), ' Casos confirmados totales'),  
           icon = "fa-arrow-up",
           color = 'orange')
} else {
  valueBox(paste0(format(sum(dep$pos.new, na.rm = T), big.mark = ","), ' Casos confirmados totales'),   
           icon = "fa-arrow-down",
           color = 'teal')
}
```

### `r paste0(format(sum(dep$pas, na.rm = T), big.mark = ","), ' Fallecidos en las últimas 24 horas')`

```{r}
if (sum(dep$pas.new, na.rm = T) > sum(y.dep$pas.new, na.rm = T)) {
  valueBox(paste0(format(sum(dep$pas.new, na.rm = T), big.mark = ","), ' Total de fallecidos'), 
           icon = "fa-arrow-up",
           color = 'orange')
} else {
  valueBox(paste0(format(sum(dep$pas.new, na.rm = T), big.mark = ","), ' Total de fallecidos'), 
           icon = "fa-arrow-down",
           color = 'teal')
}
```


### Tabla por región {.bg}
```{r}
dep %>% 
  select(Region = dep,
         Casos = pos,
         Fallecidos = pas,
         Pruebas = smp) %>% 
  arrange(desc(Casos)) %>% 
  st_set_geometry(NULL) %>%  
  DT::datatable(options = list(
    bPaginate = FALSE, 
    dom = 't'), 
    rownames = F) %>% 
  formatStyle(columns = c('Region', 'Casos', 'Fallecidos', 'Pruebas'), 
              backgroundColor = 'black', color = 'white')
```

Regional {data-orientation=columns}
=====================================  


Column 1 {.tabset}
-------------------------------------

```{r}

infobutton_7 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra los casos nuevos por día (barras) y la media móvil (línea naranja) a 7 días por departamento. La media móvil muestra el valor promedio de los casos reportados en un periodo determinado.');
    }"
  )
)

colnames(deps4) <- paste(colnames(deps4), "2", sep = "_")
vars_mav_new <- deps1 %>%
  dplyr::select(Fecha,REGION,mav_new) %>% 
  dplyr::filter(Fecha == c.date) %>%
  dplyr::summarise(max = as.numeric(max(mav_new)))%>% 
  dplyr::arrange(dplyr::desc(max)) %>%
  dplyr::select(REGION) %>%
  dplyr::mutate(REGION = ifelse(REGION=="LA LIBERTAD","LA_LIBERTAD",
                                ifelse(REGION=="MADRE DE DIOS","MADRE_DE_DIOS",
                                       ifelse(REGION=="SAN MARTIN","SAN_MARTIN",REGION))))%>% 
  .$REGION

vars_pmav_new <- deps1 %>%
  dplyr::select(Fecha,REGION,pmav_new) %>% 
  dplyr::filter(Fecha == c.date) %>%
  dplyr::summarise(max = as.numeric(max(pmav_new)))%>% 
  dplyr::arrange(dplyr::desc(max)) %>%
  dplyr::select(REGION) %>%
  dplyr::mutate(REGION = ifelse(REGION=="LA LIBERTAD","LA_LIBERTAD",
                                ifelse(REGION=="MADRE DE DIOS","MADRE_DE_DIOS",
                                       ifelse(REGION=="SAN MARTIN","SAN_MARTIN",REGION))))%>% 
  .$REGION

vars <- setdiff(names(deps2), c("Fecha","tm"))

deps2 <- deps4 %>% select(-c("Fecha_2")) %>% cbind(deps2)
```

### Casos nuevos
```{r}

plots <- lapply(vars_mav_new, function(var) {
  
  plot_ly(deps2) %>%
    add_lines(x = ~Fecha, 
              y = as.formula(paste0("~", var)),
              text = paste(deps2$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == vars[length(vars)],"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(deps4[paste0(var,"_2")],na.rm = T),
                 text="2020-04-08", name="Inicio de Pruebas Rápidas",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~Fecha, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(nac3$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE)) %>%
    layout(xaxis = list(range = c(min(deps2$Fecha),
                                  max(deps2$Fecha)),
                        color = "white"),
           yaxis = list(color = "white"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)%>% 
  partial_bundle()
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Media móvil (7 días) de casos nuevos",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Número de casos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_7),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')

```


### Casos nuevos por millón

```{r}
# allCities <- deps1 %>%
#  group_by(REGION) %>%
#  plot_ly(x = ~Fecha, y = ~pmav_new) %>%
#  add_lines(alpha = 0.1, name = "Otros Departamentos", hoverinfo = "none", 
#              line = list(color = "#64889a"),
#                            width = 1)

#allCities %>%
#  filter(REGION == "LIMA") %>%
#  add_lines(name = "LIMA")

infobutton_8 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra la media móvil (línea naranja) a 7 días por millón de habitantes por departamento comparado a la misma media móvil reportada en otros departamentos. La media móvil muestra el valor promedio de los casos reportados en un periodo determinado.');
    }"
  )
)


plots <- lapply(vars_pmav_new, function(var) {
  deps1 %>%
    group_by(REGION) %>%
    plot_ly(x = ~Fecha, y = ~pmav_new) %>%
    add_lines(name = "Otras regiones", hoverinfo = "none", 
              line = list(color = "#007e7b"),
              width = 0.5,
              showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE)) %>%
    filter(REGION == ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",var)))) %>%
    add_lines(text = paste(deps1 %>% filter(REGION==ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                                           ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                                  ifelse(var=="SAN_MARTIN","SAN MARTIN",var)))) %>% dplyr::select(tm) %>% .$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == vars[length(vars)],"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE), 
              line = list(color = "#ffa600", width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(deps1$pmav_new,na.rm = T),
                 text="2020-04-08",name="Inicio de Pruebas Rápidas",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE),
                 width=2, 
                 line = list(color = "rgb(60,141,47)", 
                             width = 2, 
                             dash = "dot")
    ) %>%
    layout(xaxis = list(range = c(min(deps3$Fecha),
                                  max(deps3$Fecha)),
                        color = "white"),
           yaxis = list(range = c(min(deps1$pmav_new),
                                  max(deps1$pmav_new)),
                        color = "white",
                        title = ""),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0, y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")))
})

subplot(plots, nrows = 5, shareX = T, titleX = F,shareY=T) %>%
  layout(title = list(text = "Media móvil (7 días) - Casos nuevos por millón de hab.",
                      font = list(size = 24,
                                  color = "white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil  - Casos nuevos por millón de hab.",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white"),
                textangle = -90)),
         hovermode = "all",
         hoverdistance = 100000000,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=65)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_8),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')


```


### Casos nuevos desde fecha de reporte
```{r}
infobutton_9 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra la media móvil (línea naranja) a 7 días desde el día del primer reporte de casos por departamento comparado a la misma media móvil reportada en otros departamentos  La media móvil muestra el valor promedio de los casos reportados en un periodo determinado.'); }"
  )
)


plots <- lapply(vars_mav_new, function(var) {
  deps1 %>%
    group_by(REGION) %>%
    plot_ly(x = ~dias, y = ~mav_new) %>%
    add_lines(name = "Otras regiones", hoverinfo = "none", 
              line = list(color = "#007e7b"),
              width = 0.5,
              showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE)) %>%
    filter(REGION == ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",var)))) %>%
    add_lines(text = paste(deps1 %>% filter(REGION==ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                                           ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                                  ifelse(var=="SAN_MARTIN","SAN MARTIN",var)))) %>% dplyr::select(dias) %>% .$dias, "días desde el primer reporte"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == vars[length(vars)],"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE), 
              line = list(color = "#ffa600", width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(deps1$pmav_new,na.rm = T),
                 text="2020-04-08",name="Inicio de Pruebas Rápidas",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == vars[length(vars)],TRUE,FALSE),
                 width=2, 
                 line = list(color = "rgb(60,141,47)", 
                             width = 2, 
                             dash = "dot")
    ) %>%
    layout(xaxis = list(range = c(min(deps3$Fecha),
                                  max(deps3$Fecha)),
                        color = "white"),
           yaxis = list(range = c(min(deps1$pmav_new,
                                      max(deps1$pmav_new))),
                        color = "white",
                        title = ""),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0, y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         font = list(color = "white")))%>% 
  partial_bundle()
})

subplot(plots, nrows = 5, shareX = T, titleX = F,shareY=T) %>%
  layout(title = list(text = "Media móvil (7 días) - Casos nuevos desde primer reporte",
                      font = list(size = 24,
                                  color = "white")),
         annotations = list(
           list(text = "Días desde primer reporte de casos en cada Región",
                x = 0.5,
                y = -0.065,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Casos nuevos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white"),
                textangle = -90)),
         hovermode = "all",
         hoverdistance = 100000000,
         dragmode="pan",
         margin = list(l=75, r=0, b=25, t=65)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_9),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')

```

Columm 2 {data-width=300}
-------------------------------------

### Infograma {.bg}

```{r}
# dep %>% 
#   st_set_geometry(NULL) %>% 
#   select(dep, pos) %>% 
#   mutate(pos = as.integer(round((pos/sum(pos))*100))) %>% 
#   waffle(rows = 5, title = "Your basic waffle chart")
# library(extrafont)
# library(emojifont)
# library(sysfonts)
# "C:/Users/Jorge Ruiz/Desktop/fontawesome-webfont.ttf"
# "C:/Windows/Fonts/fontawesome-webfont.ttf"
# font_add("FontAwesome", regular = "C:/Users/edgar/Desktop/font-awesome-4.7.0/fonts/fontawesome-webfont.ttf")
# font_import("C:/Windows/Fonts/fontawesome-webfont.ttf")
# load.fontawesome(font = 'C:/Users/edgar/Desktop/font-awesome-4.7.0/fonts/fontawesome-webfont.ttf')
# load.fontawesome(font = "C:/Users/edgar/Desktop/font-awesome-4.7.0/fonts/FontAwesome.otf")


#install.packages('extrafont')
# library(extrafont)
# library(waffle)
# loadfonts(device = "win")
# 
# waffle(c(50,20), rows = 5, title = "Your basic waffle chart", 
#        use_glyph = "male",glyph_size=10)

library(hrbrthemes)
library(ggwaffle)
library(waffle)
library(waffle)
library(extrafont)
loadfonts(device = "win")


deps %>% 
  mutate(REGION = ifelse(REGION =="LIMA" | REGION =="CALLAO", "Lima Metropolitana", "Otras Regiones")) %>% 
  group_by(REGION
  ) %>% 
  dplyr::summarize(max = sum(max(Positivos_totales))
  ) %>%
  dplyr::mutate(max = round(max/sum(max)*100),
         REGION = as.factor(REGION)
  )%>%
  ggplot(aes(label = REGION, values = max)) +
  geom_pictogram(n_rows = 20, aes(colour = REGION), flip = TRUE, make_proportional = T,
    family = "FontAwesome", size =10) +
  scale_color_manual(
    name = NULL,
    values = c("#0e5871", "#ffa600"),
    labels = c("Lima Metropolitana 92%", "Regiones 8%")
  ) +
  scale_label_pictogram(
    name = NULL,
    values = c("male", "male"),
    labels = c("Lima Metropolitana 92%", "Regiones 8%")
  ) +
  theme_ipsum_rc(grid="") +
  theme_enhance_waffle() +
  theme(legend.key.height = unit(2.25, "line")) +
  theme(legend.text = element_text(colour = "white"))+ theme(plot.background = element_rect(fill = "black"))+
    theme(plot.margin = unit(c(0,0,0,0), "cm"))


```

### Tabla por región {.bg}
```{r}
dep %>% 
  select(Region = dep,
         Casos = pos,
         `Casos nuevos` = pos.new,
         Fallecidos = pas,
         `Fallecidos nuevos` = pas.new,
         Pruebas = smp) %>% 
  arrange(desc(Casos)) %>% 
  st_set_geometry(NULL) %>%  
  DT::datatable(options = list(
    bPaginate = FALSE, 
    dom = 't'), 
    rownames = F) %>% 
  formatStyle(columns = c('Region', 'Casos', 'Casos nuevos', 'Fallecidos', 'Fallecidos nuevos', 'Pruebas'), 
              backgroundColor = 'black', color = 'white')
```









América Latina 
=====================================  


Column 1 
-------------------------------------


### Casos Nuevos {.bg}

```{r}



infobutton_10 <- list(
  name = "Información",
  icon = list(
    path = icon_svg_path,
    transform = "scale(0.84) translate(-1, 0)"
  ),
  click = htmlwidgets::JS(
    "function(gd) { 
      alert('Muestra la media móvil (línea naranja) por país comparado a la misma media móvil reportada en otros países de América Latina. La media móvil muestra el valor promedio de los casos reportados en un periodo determinado.');
    }"
  )
)
LATAM <- LATAM %>%
  group_by(location) %>%
  dplyr::mutate( mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6))  

  vars_latam_mav <- LATAM %>%
  dplyr::select(date,location,mav_new) %>% 
  dplyr::filter(date == c.date) %>%
  dplyr::summarise(max = as.numeric(max(mav_new)))%>% 
  dplyr::arrange(dplyr::desc(max)) %>%
  dplyr::select(location)%>% 
  .$location


plots <- lapply(vars_latam_mav, function(var) {  
  

LATAM %>%
  group_by(location) %>%
  plot_ly(x = ~date, y = ~mav_new)%>%
  add_lines(name = "Otras regiones", hoverinfo = "none", 
            line = list(color = "#007e7b",
            width = 0.7),
            showlegend = ifelse(var == vars_latam_mav[length(vars_latam_mav)],TRUE,FALSE))%>%
  filter(location == var) %>%
  add_lines(text = var,
            hovertemplate = paste('Fecha: %{x}',
                                  '
Media Móvil: %{y:.2f}
',
                                  '%{text}'),
            name = ifelse(var == vars_latam_mav[length(vars_latam_mav)],"Media Móvil",var),
            showlegend = ifelse(var == vars_latam_mav[length(vars_latam_mav)],TRUE,FALSE), 
            line = list(color = "#ffa600", width = 4)
  ) %>%
    layout(xaxis = list(range = c(min(as.Date("2020-02-28")),
                                  max(LATAM$date)),
                        color = "white"),
           yaxis = list(color = "white",
                        title = "", type ="log", tickmode="linear"
                        ),
           annotations = list(text = ifelse(var=="Mexico","México",
                                            ifelse(var=="Brazil","Brasil",
                                                   ifelse(var=="Peru","Perú",var))),
                              x = 0, y = 0.9,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")))%>% 
  partial_bundle()
})


subplot(plots, nrows = 3, shareX = T, titleX = F,shareY=T)%>%
  layout(title = list(text = "Media móvil de casos nuevos - América Latina",
                      font = list(size = 24,
                                  color = "white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Nuevos casos por día",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white"),
                textangle = -90)),
         hovermode = "all",
         hoverdistance = 100000000,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=65),
         yaxis = list(type="log", tickmode="linear")
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_10),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')

```



Column 2 
-------------------------------------

### Todos los paises {.bg}


```{r}

LATAM %>%ungroup() %>%
  dplyr::mutate(location = ifelse(location=="Mexico","México",
                                            ifelse(location=="Brazil","Brasil",
                                                   ifelse(location=="Peru","Perú",location)))) %>% group_by(location) %>%
  highlight_key(~location) %>%
  plot_ly(x = ~date, y = ~mav_new, text = ~location, colors = "YlOrRd",split=~location,mode="lines") %>%
  highlight(on = "plotly_hover", off = "plotly_doubleclick") %>%
    layout(xaxis = list(range = c(min(as.Date("2020-02-28")),
                                  max(LATAM$date)),
                        color = "white",
                        title ="Fecha de Reporte"),
           yaxis = list(color = "white",
                        title = "", type ="log", tickmode="linear"
                        ),
           annotations = list(text = "Media móvil de nuevos casos por país",
                              x = -0.03, y = 0.5,
                              yref = "paper",xref = "paper",
                              xanchor = "middle",yanchor = "middle",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white"),
                textangle = -90),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=65)) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T,
         modeBarButtonsToAdd = list(infobutton_10),
         displayModeBar = TRUE
  )%>% 
  partial_bundle() %>% 
  htmlwidgets::onRender('function(el, x) {
                         $("[data-title=\'Información\'] svg path").css("fill", "#f6e486");
                         $("[data-title=\'Información\'] svg").css("width","2em");
                        }')
```




# Acerca de

## Columna única

**Dashboard COVID-19 del Consorcio en Epidemiología y Ecología Espacial de Enfermedades**

Este dashboard y sus visualizaciones han sido diseñadas para asistir en el análisis de las tendencias que la pandemia de COVID-19 tiene en el Perú.

Última actualización: `r c.date`

+ Detalles técnicos 

Se utilizó la interfaz [Rmarkdown](https://rmarkdown.rstudio.com/) y el lenguaje de programación [R](https://www.r-project.org/) para producir las visualizaciones aquí presentes.

Principales paquetes utilizados

  + Tablero - [flexdashboard](https://rmarkdown.rstudio.com/flexdashboard/) 
  + Tablas - [DT](https://rstudio.github.io/DT/)
  + Mapas - [Leaflet](https://leafletjs.com/)
  + Visualizaciones interactivas - [Plotly](https://plotly.com/)
  + Manipulación de datos - [tidyverse](https://www.tidyverse.org/)


+ Fuente de datos

Los datos de Perú provienen del [Handbook Covid-19 Perú](https://jincio.github.io/COVID_19_PERU/index.html).
Esta base de datos a sido construida utilizando los [reportes del Ministerio de Salud de Perú (MINSA)](https://covid19.minsa.gob.pe/sala_situacional.asp) a nivel nacional y regional.

Los datos de América Latina provienen de [Our World in Data](https://ourworldindata.org/coronavirus) de la [Universidad de Oxford](https://www.oxfordmartin.ox.ac.uk/global-development).

+ Código fuente

La documentación y código fuente se encuentran en [github](https://github.com/ce4-peru/ce4-peru.github.io).

+ Registro de cambios

11 de Mayo de 2020 - Lanzamiento